Summary

Aboard the derelict, Marines explore the corridors, finding the Cylons dead. Athena attempts to access the derelict basestar's Hybrid, but is unsuccessful.

Some Cylons around the control center revive and advise the boarding party of the situation regarding the probe and subsequent infection of the Cylons. One of the infected Cylons, a Number Eight, addresses Athena as "traitor."

The boarding party and prisoners are en route back to Galactica when the basestar self-destructs.

Galactica quarantines the boarding party and prisoners while Dr. Cottle finds out if the virus affects humans. The human members of the boarding party are cleared while Athena is ordered to stay put, as her blood work hasn't been done. Helo is infuriated, but wants to be notified as soon as her results are available.

Dr. Cottle's investigation identifies a virus that can be treated, but not cured for Cylons. President Roslin, Admiral Adama, Lee Adama, and Helo discuss the idea of taunting the vaccine in exchange for information. A Simon is brought before them, and informs them that the entire baseship was abandoned, because resurrection would infect the others. He also mentions that Gaius Baltar provided the information on the path to Earth.

Aboard Colonial One, Lee Adama suggests a plan to eliminate the entire Cylon race by executing their prisoners in range of a Resurrection Ship, where the downloaded consciousnesses would infect the remaining Cylons, because according to Simon the virus carries a bioelectric feedback component that could spread it even through the download process. Helo scoffs at the idea, considering it genocide.

Aboard Galactica, Athena finds she's immune because of antibodies generated within her body by carrying her daughter, Hera. Helo tells her of the Fleet's plan, and Athena understands.

Admiral Adama shows slight dissent about the plan, indicating regulations that forbid him to proceed without presidential order. Despite the ethical ramifications, the President authorizes the biological attack.

Galactica jumps to a Cylon supply line, and launches Vipers and Raptors to attract the Cylon fleet. In the midst of this, Helo initiates a plan to thwart the execution, unplugging what looks like a standard power connector from an environmental control box.

The Cylons jump into the area, with Resurrection Ship in tow. Adama orders the execution of the prisoners.

Lee Adama leads a team to execute the prisoners, but finds that all the prisoners have been killed prior to the Resurrection Ship arriving. Adama orders a recall, and Galactica escapes without sustaining any major damage.

Helo converses with Athena about his actions. He maintains that what he did was right, regardless of the consequences.

Aboard Galactica, Adama reports that the prisoners were suffocated due to a failure in the environmental controls. Roslin is quick to point out one or two might be responsible, but Adama closes the issue. Subsequently, the virus was most likely an accidental exposure, similar to one reported 3000 years ago. Adama points out that they're on the right track to Earth, but Roslin notes that the Cylons are on the right track as well.

Aboard the bastestar, Baltar is being interrogated by Three and Caprica-Six, knowing about the beacon. Three and Caprica-Six imply that Baltar is connected to the virus and to Galactica. Baltar attempts to reconcile, only to be confronted by Centurions.

In his "projection", his mental Six tells him to relax. Meanwhile, his body is being subjected to torture; Caprica Six is visibly disturbed by the torture and backs away.

Baltar's torture continues as Three continues to interrogate Baltar regarding his supposed involvement with the virus. In his mind, he attemps to avert the pain by making love to his mental Six. Despite extreme pain, Baltar endures.

Notes

Fleet population is 41,420. Barring any births, there is an unaccounted loss of at least two since "Torn".

The story behind the Lion Nebula beacon and the virus may have been inspired by the lunar lander Surveyor 3. Before launching in 1967, its camera was accidentally contaminated by a common bacterium. When the camera was recovered by Apollo 12 astronauts, the microbes returned to life, having survived two and a half years of vacuum, radiation, and temperature extremes.

This is the first episode in which Saul Tigh does not appear, more than likely due to his promise to William Adama at the end of "Torn" after Adama's confrontation with both Tigh and Kara Thrace. Up to this point, the only characters to have appeared in every episode are Laura Roslin and William Adama, albeit Adama was unconscious for several episodes early in season 2.

A scene where Tigh accuses Helo of being a poor XO and having a relationship with a Cylon was not filmed at Michael Hogan's insistence, who argued that Tigh would heed Adama's order to pull himself together in the previous episode.[1]

Helo has been promoted to the rank of captain, as evident in both dialogue and costuming.

In his podcast, Moore notes that this episode shares similarities to the Star Trek: The Next Generation episode, "I, Borg", though he does not mention the episode by name. Moore also noted that this episode was brought up for discussion during the writer's meetings to discuss development of this episode, as "I, Borg" discussed using a lone Borg drone implanted with a computer virus to infect the Borg collective.

The location in space of the attempted attack on the Cylons is designated "The Region of NCD2539 Above/North."

The Cylon Hybrid does not appear in this episode despite actress Tiffany Lyndall-Knight's name appearing in the ending credits.

A scene depicted in a promotional photo showing Number Six and Three in a projected forest was cut from the episode. The scene also showed them speaking in Number Three's projection of a cathedral. The scene is included on the DVD release.

Other scenes cut from the episode include Kara Thrace interrogating a Leoben model in a callback to "Flesh and Bone" and Admiral Adama surveying the Cylon basestar in a Raptor.

Lee Adama leading the Marine boarding party is a remnant of a dropped subplot in which he joins the Marines to lose his weight and become a soldier again[2].

This episode confirms that Sharon/Athena is no longer living in her cell, likely due to her having now been given a commission. Her former cell is in fact used to house the infected Cylons, and the furnishings present when it was last seen in "Occupation" have been removed.

Gaeta briefly becomes XO of Galactica during the aborted extermination mission when Helo asks to be relieved. This and the fact he is seen in uniform indicates that he is once more an officer (a position he did not have in "Collaborators").

When Helo suggests the Cylons don't deserve genocide because they tried to live with humans on New Caprica, Roslin counters that he wouldn't know anything about New Caprica because she doesn't remember him ever setting foot on the planet. In fact, Helo is seen on New Caprica in flashbacks during "Unfinished Business." Helo does not correct the President on this omission.

Roslin may be experiencing selective memory, or she may not have seen him there.

Perhaps she was referring to spending time on the planet during the occpation though Roslin should know that doing so would have been nearly impossible.

Galactica's marine team encounters a fleet of dead Cylon raiders cluttering the airspace around the adrift basestar, so much so that Apollo's raptor has to nudge a few raiders out of the way to fly into the entryway. In the previous episode, Baltar's raptor, flying to the same basestar, encounter no additional derelict ships, and had a clear path into the basestar's landing bay. Could the dead raiders simply have ejected from their launch slots after Baltar left?

Analysis

The disease

The Cylons could have cured themselves of this plague relatively quickly, if Galactica had succeeded in infecting them. It is quickly noted in the episode that Sharon Agathon is herself immune because fetal cells from Hera created effective antibodies against the virus. Hera is immune to the virus because she is a hybrid Human-Cylon. Now that she is in custody of the Cylons, Baltar could have utilized her immunity, as he previously did on Roslin, as capital to further his self-preservation amongst them.

It can be assumed that executing the captured Cylons will send them back to the Resurrection Ship, thus infecting the Cylon network.

For the Cylons to study the plague they would have become infected themselves, therefore, there was no way they could have tried to find a cure without potentially perishing

The wider implications of such an event could be religiously meaningful to the Cylons. Cylons have time and again shown religious deference by sometimes overlooking rational explanations. By saving the Cylon race Hera could have been elevated to messiah status, if her very creation has not already ordained her as one to the Cylons because their God proclaimed her creation.

The presence of Hera is profound enough to the Cylons, which could be preventing them from seeing that Hera could be used as a tool.

There is a fundamental flaw in the plan Lee Adama develops: Even if the virus successfully infects the Resurrection Ship, the other Cylons would isolate that individual ship, thus preventing a widespread epidemic. The resulting impact on the Cylon fleet would be no greater than previous destruction of the Resurrection Ship in "Resurrection Ship, Part II".

Apollo's plan is based on an account of the Cylon analysis of the threat. He could simply assume they are correct and that the virus can spread like wildfire from one Resurrection Ship to another.

Also, by infecting a greater mass of ships, Galactica could board the ships, take much needed resources and more infected Cylons for further use as biological weapons.

The science behind the virus is somewhat questionable. While the biological aspect is sound, the existence of a "bioelectrical feedback component" appears to be technobabble. It would be impossible for a biological virus (i.e. a physical pathogen) to be transmitted by download to the Resurrection Ship. Such a feedback - scrambling the brainwave patterns - could disrupt the download process, but it is unclear how it could spread the virus itself on the other side. It simply may be a case of Cylon superstition, which is known to happen from time to time.

From Dr. Cottle's dialogue, it would appear that the problem lies with how the Cylons' immune systems reacts with the virus, more than the virus itself. If this is the case, it is likely that the immune system's reaction would carry through the download and possibly be passed to other Cylons throughout the network.

Conceptually, there is actually very little difference between a physical and a computer virus. Both usurp cell function. Moreover, if the virus is a retrovirus, its genome (be it physical or digital) will be transcribed into the cellular DNA, which might be downloaded to the Resurrection Ship.

That the Centurions and Raider are disabled as as well might hint at a digital component, but in "Torn" it is noted that the Centurions shut down as soon as the Hybrid became infected. This indicates that the Hybrid is in some sort of contact with the Centurions. Moreover, Raiders are partly biological and could be infected in their hangars.

Dr. Cottle explains that Cylons carry antibodies that break down the RNA of his proposed vaccine. However antibodies have no disintegrative functionality, and only prime recognized pathogens for phagocytosis, though he may have simplified the explanation. But as vaccines are developed from the pathogenic organism (or a close relative) it would be impossible for the Cylons to carry antibodies specific for the vaccine RNA (or for the products it encodes) or otherwise they would be immune to the pathonogenic virus itself.

The genetic pool the Cylons were created from may predate the human immunity to the plague from just a couple hundred years ago, yet the Cylons, even as a class of machines, are only 40 to 60 years old. This may indicate another, non-Colonial, source for the DNA.

There is. The humanoid Cylons were created by the Five, who are two thousand years old.

None of the four members of the Five who are in the fleet at this time are shown to be exposed to the infected Cylons.

It seems this virus could also be a fairly reliable (although not conclusive) litmus test for Cylons in the Colonial Fleet.

It seems reasonable to assume that all members of Galactica's boarding party who boarded the baseship are not Cylons, save Sharon Agathon.

Baltar's boarding of the baseship does not discount Baltar from being a Cylon, as Baltar was in a self-contained flight suit the entire time he was on the basestar. Using standard biohazard procedures, he would have remained in the suit which would be disinfected from the outside before taking it off.

The environmental controls seem to be circumvented by Karl Agathon by pulling a single plug (unless this is just the last step in a longer process). One would assume that a warship has cascading fail safe systems to protect against such catastrophic failures from simple system malfunctions.

The quarantine procedures, sheets of plastic in rooms and hallways, seem ineffective. On a spaceship it should be possible to cut off selected areas from life support completely. Again, this might have been done for dramatic effect.

Dramatic effect aside, the plan could be implemented faster by having the execution squad standing by for immediate action and having the FTL drives spun up at all times.

Other

Adama's reaction to the premature death of the prisoners is yet another example of what are simultaneously his greatest virtues and most glaring flaws – his dedication to those under his command, and his need to keep his conscience clear.

In this episode, Raptors are shown loaded to the teeth with weapons systems. In the past (Miniseries, "The Hand of God"), Raptors have rarely been depicted in actual combat, preferring instead to hang back while coordinating battlefield logistics. They have been shown armed in a few prior episodes ("Kobol's Last Gleaming, Part II", "Fragged"), but this is by far their most prominent combat role to date. The Raptors are using the external missile pods and cannons introduced in "Exodus, Part I & Part II" and engage in the same maneuver used to launch the decoy drones during the Battle of New Caprica.

Baltar calls the Number Three torturing him "D'Anna", to which she responds. However, this is not the reporter copy that hid in the Fleet. She is the same copy that was on Caprica trying to box Caprica Six and Boomer before Caprica Six killed her (Downloaded): It is shown that she is the same as the one having dreams on New Caprica, who in turn is identified as the "Downloaded" copy.

Gaeta is surprised to hear that Baltar is alive, even though he was there when Number Three offered Baltar evacuation from New Caprica. Therefore, Gaeta likely assumed that Baltar has not survived as Baltar went off to forcefully prevent the nuclear detonation on New Caprica, thus betraying the Cylons. Therefore Baltar would have little chance of survival at the hands of the Cylons, let alone being their "guest". It should be noted that extenuating circumstances, such as Baltar's rescue of Hera and his aid in helping the Cylons find the road to Earth are the main reasons why the Cylons let him exist on the basestar.

In a deleted scene Apollo says they need everyone in the air for this mission, including those who would normally not have flight status. As he says this he (and the camera) looks right at Starbuck indicating he was talking about her. This clarifies that Thrace is still officially grounded after the events of "Torn".

Adama cites the danger of the disease as an excuse to not bring the beacon to Galactica, despite Cottle's request. The beacon is subsequently destroyed when the basestar self-destructs. This sequence covers a potential plot hole involving the beacon ... considering its relationship to the 13th tribe, the beacon would have been of great interest to the fleet, and would have raised the question of why more time in the episode wasn't devoted to studying it. Instead, the fleet loses a valuable clue, making their road to Earth more difficult. Still, Adama's excuse about the disease is rather flimsy, though he didn't know the ship would blow up and he probably thought they could retrieve the beacon later after the quarantine issue was cleared up.

Questions

Answered Questions

Will there be any consequences of the sabotage for the Agathons from other crewmembers who may figure they are behind said sabotage? How will this affect Karl Agathon's reputation as a Cylon-lover or his credibility as XO? (Answer)

Is Karl Agathon's act of sabotage and his view that the Cylons did attempt to co-exist with humans the beginnings of a more conscious act of betrayal to the Fleet, thus following a similar pattern as how Sharon Agathon eventually switches sides. Would Karl thus become like Sharon and eventually identify himself with the Cylons? (Answer)

Why does Baltar take photos of the suspicious object and claim to have seen nothing suspicious? Doesn't he realize the Cylons would review the documentation he sends and immediately discover his lie?

Baltar was unaware he had taken a photo of it; he never intentionally photographed the beacon while on the baseship in Torn, and Caprica Six had to zoom in on an edge of one of his pictures in order to find the image of the beacon.

Unanswered Questions

Where is Caprica-Six's own internal Baltar in all of this?

Of the Cylons, which type tells the basestar to self-destruct: The Hybrid or a humanoid Cylon? Considering her odd look after the destruction, might it be Sharon Agathon?

When the basestar self-destructs, is it an indicator that the Hybrid on the ship has died, thus no longer able to maintain the integrity of the ship?

If the basestar and the virus do represent a true genocide threat to the Cylons why do they just leave them to slowly expire instead of destroying the ship right away?

What kind of new start are the Cylons planning for Earth? Just a new home planet, an attempt at human Cylon relations not tainted by the destruction of the Twelve Colonies, or something else?

Would the possible presence of this new pathogen on Earth, if indeed it was left by the Thirteenth Tribe, mean that Earth is no longer a viable planet for the Cylons? Would any Cylons landing on Earth again be susceptible to this virus?

Why does an entire Cylon fleet (including a Resurrection Ship) jump to the encounter with Galactica? Why is the Resurrection Ship not left behind somewhere else, as it was done in previous battles?

Does Number Three love Baltar?

Why does Simon so quickly claim science can not provide a solution to the infection?

Will Sharon's words to Karl about her commitment to keep her word stay true should she ever discover that Hera is alive? Will she live up to her promise to Adama and the Fleet?

Is it possible that while torturing Baltar, Number Three actually believes that God is talking to her through Baltar (similar to him being the hand of God)? When he says "I want you to believe in me! don't stop, please don't stop - you're all I have left - I believe in you - I love you - with all my heart I love you" it is possible that this may give Three the reassurance she needs that she is on the right track.

After discovering that the virus does not affect humans, why does Karl Agathon remain outside the isolation area instead of comforting his wife in person?

Why do the boarders of the basestar not recognize the symptoms of disease in the dying Cylons before being told so by a Cylon?

It should be noted that there is nobody with a medical background in the boarding party, which might have something to do with it.

Official Statements

Lawless: "The difficulty was I had to pretend to not be hearing Six who was sitting right beside us carrying on a conversation with him. I was supposed to be completely unaware of this sort of cyber sex relationship, and yet I could hear her and it was a little annoying. In particular when the camera is on you; just let it be your scene, but I didn’t want to break James [Callis]’ spell by asking for things to be changed."[3]

Noteworthy Dialogue

On Colonial One:

Karl Agathon: Genocide? So that's what we're about now?

Lee Adama: They're not human! They were built, not born. No fathers, no mothers, no sons, no daughters--

Three: There's no such thing as coincidence. God wills the universe according to his design.

Gaius Baltar: I'm a scientist. And as a scientist, I believe that if God exists our knowledge of him is imperfect. Why? Because the stories and myths we have are the products of men. The passage of time. That religion in practice is based o­n a theory. Impossible to prove. Yet you bestow it with absolutes like, "There is no such thing as coincidence."

Baltar: Absolute belief in God's will means there's a reason for everything. Everything! And yet you can't help ask yourself how God can allow death and destruction and then despise yourself for asking. But the truth is, if we knew God's will, we'd all be Gods, wouldn't we? I can see it in your eyes, D'Anna. You're frustrated. You're conflicted. Let me help you. Let me help you change. Find a way to reconcile your faith with fact. Find a way towards a rational universe.